Missing necessary library for svSolver in May 2023 release

[JohnDLee]

Describe the bug
After updating to the newest version of Simvascular, I encountered a problem generating data files for simulation using svpre. It appears a c library is missing from the installation.

To Reproduce
Steps to reproduce the behavior:

1. Download May 2023 Simvascular and have July 2022 (latest) svSolver
2. Open Simvascular and create a 3D simulation job.
3. Click on "Create Data Files for Simulation"
4. Wait for a bit and error should pop up.

Expected behavior
After clicking generate files for simulation, I expect it to process for a while, then generate bct, geombc, and restart files. However, it fails to generate files.

Error Message

dyld[22928]: Library not loaded: /usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib
Referenced from: <7F8D4F10-902B-3ADE-B253-9A20D4A22593> /usr/local/sv/svsolver/2022-07-22/bin/svpre
Reason: tried: '/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/svExternals/lib/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/svExternals/lib/plugins/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/./libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/bin/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/lib/plugins/libgfortran.5.dylib' (no such file), '/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

Desktop (please complete the following information):

• OS: MacOS Ventura 13.2
• SimVascular Version - May 2023

Additional context
The problem does not occur in the July 2022 release, suggesting that the missing library exists in the that release, but not the May 2023 one. I suspect if the libgfortran.5.dylib already exists on certain OS's then this problem would not be encountered.

[ktbolt]

@JohnDLee The 2022-02-07 release of svSolver was built with GCC 11.3.0 so it will be looking for /usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib

Which gcc version do you have installed?

[JohnDLee]

Hmmm, I just don't have the gcc directory at all in my /usr/local/opt/ directory

[ktbolt]

I think that /usr/local/opt/gcc/ was just the last place the OS loader looked trying to find the libgfortran.5.dylib library.

Note that the latest MacOS versions have completely diverged from other Linux versions from where system libraries are located. I've seen some hideous solutions to this problem on the web.

The svSolver install actually has the libgfortran.5.dylib in /usr/local/sv/svsolver/2022-02-07lib so you can copy it so the OS can find it like so

mkdir $HOME/lib directory
cp /usr/local/sv/svsolver/2022-02-07lib/libgfortran.5.dylib $HOME/lib

[dkp]

In an Ubuntu singularity container, I get a similar message for svSolver:
"/usr/local/sv/svsolver/2022-07-22/bin//svsolver-nompi: error while loading shared libraries: libvtkIOXML-7.1.so.7.1p: cannot open shared object file: No such file or directory"

I looked in /usr/local/sv/svsolver/2022-02-07/lib (and bin) and did not see libgfortran.5.dylib.
/usr/local/opt does not exist.

Any suggestions?

[estamos]

I am currently facing the same error in SimVascular 2023.05.23.

• svSolver-macOS-BigSur-2022-07.pkg Installed
• OS: MacOS Sonoma Version 14.1.2 (23B92)
• gcc --version Apple clang version 15.0.0 (clang-1500.0.40.1)

I am trying to locate libgfortran.5.dylib in my system with no success so far.

Description
When I am trying to Create Data Files for Simulation for a Chosen Mesh I receive the following:

⚠️ Failed to finish creating data files.

dyld[5780]: Library not loaded: /usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib Referenced from: <7F8D4F10-902B-3ADE-B253-9A20D4A22593> /usr/local/sv/svsolver/2022-07-22/bin/svpre Reason: tried: '/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/svExternals/lib/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/svExternals/lib/plugins/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/./libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/bin/libgfortran.5.dylib' (no such file), '/Applications/SimVascular.app/Contents/Resources/lib/plugins/libgfortran.5.dylib' (no such file), '/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/usr/local/opt/gcc/lib/gcc/11/libgfortran.5.dylib' (no such file), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

Any help or tip would be appreciated.

[myadav5]

Hello,
I too am having exactly the same error as dpk on this thread.

Error message :

To reproduce:

1. Click on 'Create Data Files for Simulation' (once you have your simulation setup ready)
2. Click on 'Run Simulation' with certain number of processor with 'Use MPI' checked in.

Platform : Ubuntu 22.04

SimVascular Version : 2023.03.27

Looking forward to suggestions.

Thank you